Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

doi:10.1128/CMR.14.3.547-560.2001

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Clinical Microbiology Reviews, July 2001, p. 547-560, Vol. 14, No. 3
0893-8512/01/$04.00+0 DOI: 10.1128/CMR.14.3.547-560.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

Alex van Belkum,¹^,^* Marc Struelens,² Arjan de Visser,³ Henri Verbrugh,¹ and Michel Tibayrenc⁴

Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center Rotterdam, 3015 GD Rotterdam,¹ and Laboratory of Microbiology Wageningen Agricultural University, 6703 CT Wageningen,³ The Netherlands; Department of Microbiology Université Libre de Bruxelles Hôpital Erasme, Brussels, Belgium²; and Centre d'Etudes sur le Polymorphisme des Micro-Organismes, UMR CNRS/IRD 9926, Génétique Moléculaire des Parasites et des Vecteurs, IRD, 34032 Montpellier Cedex 1, France⁴

Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy,research aimed at elucidation of evolutionary dynamics or phylogeneticrelationships, population genetics of microorganisms, and microbialepidemiology all rely on genetic typing data for discriminationbetween genotypes. Apart from being an essential component ofthese fundamental sciences, microbial typing clearly affects severalareas of applied microbiogical research. The epidemiological investigationof outbreaks of infectious diseases and the measurement of geneticdiversity in relation to relevant biological properties such aspathogenicity, drug resistance, and biodegradation capacitiesare obvious examples. The diversity among nucleic acid moleculesprovides the basic information for all fields described above.However, researchers in various disciplines tend to use differentvocabularies, a wide variety of different experimental methodsto monitor genetic variation, and sometimes widely differing modesof data processing and interpretation. The aim of the presentreview is to summarize the technological and fundamental conceptsused in microbial taxonomy, evolutionary genetics, and epidemiology.Information on the nomenclature used in the different fields ofresearch is provided, descriptions of the diverse genetic typingprocedures are presented, and examples of both conceptual andtechnological research developments for Escherichia coli are included.Recommendations for unification of the different fields throughstandardization of laboratory techniques aremade.

^* Corresponding author. Mailing address: Department of Medical Microbiology & Infectious Diseases, Erasmus University MedicalCenter Rotterdam (EMCR), Dr. Molewaterplein 40, 3015 GD Rotterdam,The Netherlands. Phone: 31104635813. Fax: 31104633875. E-mail:vanbelkum{at}bacl.azr.nl.

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